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- PDB-8ye0: Crystal structure of KgpF prenyltransferase -

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Basic information

Entry
Database: PDB / ID: 8ye0
TitleCrystal structure of KgpF prenyltransferase
ComponentsLynF/TruF/PatF family peptide O-prenyltransferase
KeywordsTRANSFERASE / ripp / prenylation / prenyltransferase / abba fold
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / TRIHYDROGEN THIODIPHOSPHATE / LynF/TruF/PatF family peptide O-prenyltransferase
Function and homology information
Biological speciesMicrocystis aeruginosa NIES-88 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHamada, K. / Inoue, S. / Goto, Y. / Suga, H. / Ogata, K. / Sengoku, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands.
Authors: Inoue, S. / Thanh Nguyen, D. / Hamada, K. / Okuma, R. / Okada, C. / Okada, M. / Abe, I. / Sengoku, T. / Goto, Y. / Suga, H.
History
DepositionFeb 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LynF/TruF/PatF family peptide O-prenyltransferase
B: LynF/TruF/PatF family peptide O-prenyltransferase
C: LynF/TruF/PatF family peptide O-prenyltransferase
D: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,80516
Polymers136,0994
Non-polymers1,70612
Water6,359353
1
A: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4514
Polymers34,0251
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4514
Polymers34,0251
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4514
Polymers34,0251
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4514
Polymers34,0251
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.681, 69.344, 86.426
Angle α, β, γ (deg.)109.115, 93.102, 104.888
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
LynF/TruF/PatF family peptide O-prenyltransferase


Mass: 34024.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa NIES-88 (bacteria)
Gene: EWV68_12770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A551Z2V8
#2: Chemical
ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: PEG2000MME, Bis-Tris, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.94→43.64 Å / Num. obs: 69214 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.38 Å2 / CC1/2: 0.967 / Net I/σ(I): 7.7
Reflection shellResolution: 1.94→1.98 Å / Num. unique obs: 4404 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MrBUMPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→43.64 Å / SU ML: 0.2641 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.4017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 1996 2.89 %
Rwork0.1908 67146 -
obs0.1922 69142 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.21 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9203 0 96 353 9652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00389497
X-RAY DIFFRACTIONf_angle_d0.721512869
X-RAY DIFFRACTIONf_chiral_restr0.05081402
X-RAY DIFFRACTIONf_plane_restr0.0051663
X-RAY DIFFRACTIONf_dihedral_angle_d6.61211311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.37671340.2724747X-RAY DIFFRACTION94.63
1.99-2.040.24591530.23844726X-RAY DIFFRACTION97.21
2.04-2.10.27071400.22824703X-RAY DIFFRACTION95.86
2.1-2.170.29311380.22124763X-RAY DIFFRACTION96.27
2.17-2.250.28621390.22784760X-RAY DIFFRACTION97.53
2.25-2.340.29241470.2154766X-RAY DIFFRACTION97.13
2.34-2.440.27571420.21884788X-RAY DIFFRACTION97.22
2.44-2.570.30781410.21694799X-RAY DIFFRACTION97.53
2.57-2.730.27931320.21174819X-RAY DIFFRACTION97.87
2.73-2.950.27031450.21014821X-RAY DIFFRACTION98.28
2.95-3.240.2591530.1974817X-RAY DIFFRACTION98.09
3.24-3.710.22011410.17464883X-RAY DIFFRACTION98.94
3.71-4.670.19541420.15384860X-RAY DIFFRACTION98.87
4.67-43.640.18521490.16544894X-RAY DIFFRACTION99.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.67000786934-6.41624704403-3.222787519316.822382580932.555743061053.13502180509-0.1497736035860.208048580524-0.962742428985-0.096945678265-0.1965257211220.6756778006850.3510845772160.04199578816350.3070847758830.241667832809-0.0492940653312-0.04758021721910.235427023146-0.01563075633110.582243341663-3.38423797066-30.438347572327.0922242793
23.02879444226-0.660420624689-1.273599515151.719013403090.6871394203682.323197074220.08309212125780.233873894293-0.241198259992-0.316812318435-0.2020004435270.2634480062020.0183704700028-0.1773274113520.07273617511970.2186713781920.0407281110876-0.09815620691250.192436531604-0.01886179908920.2670164022671.85833100996-19.145377921915.4085760108
31.290621815880.01387574412361.072726995061.309074767860.7395318454233.371281662770.0508809677276-0.03814314254440.0817147067333-0.1322795064460.0480608152023-0.213722909992-0.0878743161660.253175636859-0.0853041056680.139192348406-0.0074153907924-0.01313096663350.1929466149890.01424594979940.24656448610717.8584314142-9.741695506124.0809281536
43.26753045272-0.6743829292440.3799155898972.311451196710.6248168922425.197238936320.0680996841566-0.302163670231-0.140712200378-0.00418068107764-0.02623816301810.2622955556350.186913204013-0.2592418458470.003852685381840.128656173697-0.016918622943-0.04100862420230.2121215583070.007537842295490.2231056286414.66606387807-12.072416223335.0923800576
54.58225921568-1.83071657935-0.6362501469476.351189961411.609101721561.718615389370.150591008972-0.02276306124810.000391064458380.5404446764870.038108167433-0.608973056865-0.05500834436520.278348967699-0.1443985738890.240791934409-0.052932545196-0.08621649423470.247535404254-0.07274348064130.29441547374711.7424506479-30.2950032215-13.584633175
63.646163663240.687542703855-0.4026394394972.750890976930.3964526062633.443522822760.0814170982357-0.2084460241270.3881849943390.330268773326-0.00747338140835-0.0603256139293-0.402653605585-0.0158906495977-0.04021102183060.2565521009560.000448759340045-0.0530028394920.171991193408-0.03571535400180.221383995612-2.71742898908-25.2052154956-11.0551824592
74.501204761822.34737794741.676305581934.129421040082.255141325252.45805349408-0.0858112024332-0.1892331563060.498091424554-0.194993942435-0.129756713630.319673519129-0.236584318129-0.4651877173980.1821658320460.2326997578740.06298645532-0.03899589613460.2601064952250.000885954100680.209285986451-15.5411608451-27.9277783775-18.144649743
86.26872811123-0.06246228714760.2767551306911.782933402320.8629826161553.816156848510.0954385852470.4780511694-0.3790137543190.0335547505308-0.09276330232630.114153300212-0.071712930262-0.188586176267-0.0193029587860.18698782149-0.0190224157894-0.04612278793830.258538006122-0.006122013996060.158340070889-11.6632646979-38.7930199924-28.9829025366
94.699896492-0.6504455496592.898756055644.38996129654-0.9940586050935.885423413650.01589867217630.480527520723-0.115115527231-0.04012818654460.122051110825-0.190570312829-0.1539060857920.522924027935-0.1240711467810.179071165639-0.0644187404451-0.02116085589090.224564860484-0.04468795691550.1915484185851.73701865118-36.7674098119-28.6495300858
100.793207839930.5949933042160.5982196505392.01435485579-0.04993680374672.78583786652-0.2387429575130.470838891635-0.155038884851-0.3336498272670.7045485214320.2485465611190.56805247229-0.452268217484-0.5036459254450.475591420279-0.119148409225-0.0005603048520710.4235967284370.02804604888260.358318169436-31.504463657314.0934314575-8.35138406537
110.997125886914-0.207426220446-0.4891186555390.858019058567-0.661762825252.94491008856-0.2561592594260.14920680327-0.3397411935460.1571179199240.1783096743960.3881645219020.81262378143-0.64189858109-0.1686703424780.992906861437-0.305620259520.1472684326360.5624164144640.2339613518110.201161525724-27.3229810826.199794047670.854146454402
122.137117669090.592444943639-1.073297965981.6219779593-1.180427690731.09739744831-0.0693219492992-0.154505502015-0.157963327540.7226569171650.138863516325-0.2329155649910.85068589969-0.0373962912097-0.1006404527760.861650226884-0.0921033318851-0.1476864556480.3503216970070.0538149083390.350193520543-19.14914409428.71377876609-4.48630485322
131.39560273224-1.451178945120.01207425857012.83238918537-1.845268460512.56998794818-0.0519198056007-0.295492043414-0.4373989014350.6979006841270.106025531703-0.9160525315280.775822701491-0.06578307576260.2652516270670.884838454619-0.0450049800058-0.2578638783460.3055460477660.05455442899960.497392119-10.72468782165.59332483037-3.71470720193
141.886287025170.2259412057210.6692711360582.65776830612-1.705058989581.50339192805-0.1092400564440.143350680676-0.282364784318-0.339303468592-0.126350488911-1.528759145011.16084027610.7915837144890.44678157731.008360826560.185916530382-0.0220920796850.2504284655940.03457837164470.844323980332-5.78601189833.70199321648-15.3676312449
151.943267135830.339706505129-0.2933290476455.70138323626-1.179671656082.04010793354-0.3678964337130.737571084297-0.639707523687-1.426894517220.265619615921-0.87499349311.41269962122-0.213310172249-0.08803093874021.23740905752-0.2334959720010.1068588970160.453793184401-0.1117374954750.51193276299-16.00960587491.08988060123-27.7216708511
163.057367191621.37657792512-1.198634361574.557102602881.097455295341.864404542830.1546650979840.02754585398030.134406934446-0.1069239727670.05517015732661.467552446790.751415516821-1.06175411548-0.1317605558560.818635227819-0.476401920523-0.178360405560.8197295611950.09073019015060.621062477725-35.04691691941.81849837919-19.5140020378
173.396984241140.4044309549380.4980811209963.9758761853.769554175763.59631115396-0.00168484691093-0.00622745656851-0.264486040211-0.490901810440.262440402176-0.453177992640.561747547431-0.0160442802041-0.2241995237281.10994575363-0.263671831003-0.08284953358480.390194623520.06271887600090.331210566281-22.2793093992-1.04631875056-20.6157233811
183.3967057168-1.194655782730.4900474826015.86102029906-0.2602490460915.647787432170.4116720656420.3525003321780.284449262428-0.620295446556-0.466687378358-0.524357084402-0.07231922824050.1373112510870.02827884227170.2595598810340.038949348530.05099426165090.1986238781660.06180077633790.3426759166887.5139644417225.978933710616.8800009587
192.43352906557-0.28034757178-0.1630944465914.07660045027-0.5523040440812.216120769570.2381394712080.578302456193-0.778253055931-0.555399691396-0.3310062555880.8155515862730.42083344611-0.1097384702070.05480813975680.3728481957790.0422734098364-0.1405395714850.242086195572-0.1414662989870.619559925515-1.7273410059712.445004601417.861694354
202.23025308244-0.877889355512-0.6675910036985.43783502147-0.4537857799331.00810820898-0.0766743044664-0.382674227885-0.6878700679470.9072516561730.2338399811491.114579517040.225177628035-0.404131056165-0.1158140393390.5737919067290.005300630403970.2441935869670.3862328728610.3042552757011.05220405722-10.899636072611.013037967235.3566455351
213.19871690242-1.81805572742-0.1122688087793.802124724250.5625580156362.29303269837-0.367295390819-0.6183532468670.165205465910.7948545258960.352597620566-0.0550017580637-0.05150287353880.08568519096780.0247562356780.3682212128180.066729023545-0.06388285738020.2637966315730.01028805243110.31765312522-0.18104371091725.001653943635.1805588996
226.65970318596-2.477183435654.417459767393.71508276157-1.773584907347.26293372978-0.151876661606-0.475876763413-0.003021024198830.4590576347190.410910710338-0.3737496858740.2357067371980.212731950245-0.1816375058250.3490566496870.100345882292-0.1738941678140.281978524319-0.07341866645910.4553867290126.2889205350925.969752354335.0387966141
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 25 )AA3 - 251 - 23
22chain 'A' and (resid 26 through 141 )AA26 - 14124 - 139
33chain 'A' and (resid 142 through 224 )AA142 - 224140 - 222
44chain 'A' and (resid 225 through 290 )AA225 - 290223 - 288
55chain 'B' and (resid 11 through 42 )BE11 - 421 - 32
66chain 'B' and (resid 43 through 141 )BE43 - 14133 - 131
77chain 'B' and (resid 142 through 192 )BE142 - 192132 - 182
88chain 'B' and (resid 193 through 248 )BE193 - 248183 - 238
99chain 'B' and (resid 249 through 290 )BE249 - 290239 - 280
1010chain 'C' and (resid 1 through 25 )CI1 - 251 - 25
1111chain 'C' and (resid 26 through 42 )CI26 - 4226 - 42
1212chain 'C' and (resid 43 through 90 )CI43 - 9043 - 90
1313chain 'C' and (resid 91 through 141 )CI91 - 14191 - 141
1414chain 'C' and (resid 142 through 192 )CI142 - 192142 - 192
1515chain 'C' and (resid 193 through 248 )CI193 - 248193 - 248
1616chain 'C' and (resid 249 through 262 )CI249 - 262249 - 262
1717chain 'C' and (resid 263 through 290 )CI263 - 290263 - 290
1818chain 'D' and (resid 11 through 70 )DM11 - 701 - 60
1919chain 'D' and (resid 71 through 141 )DM71 - 14161 - 131
2020chain 'D' and (resid 142 through 165 )DM142 - 165132 - 155
2121chain 'D' and (resid 166 through 264 )DM166 - 264156 - 254
2222chain 'D' and (resid 265 through 290 )DM265 - 290255 - 280

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